Three years after his playing career ended, Munn got his first head coaching job at Albright College in Reading, Pennsylvania, where he stayed for two seasons (1935–1936), compiling a record of 13–2–1.[1] From 1938 to 1945, he was an assistant football coach at the University of Michigan, once again under Crisler. Munn served as head coach at Syracuse University for one season in 1946 before leaving for Michigan State. One of Munn's assistants at Syracuse was former Orangeman standout Duffy Daugherty, who followed Munn to Michigan State and assisted him there for seven seasons before succeeding Munn as head coach. Munn is one of the few people to have coached at both Michigan State and its archrival Michigan.

In 1947, Munn and the Michigan State administration, led by university president John A. Hannah, approached Notre Dame president Father Cavanaugh to have his Fighting Irish play the Spartans for the first time since 1921. MSU initially offered to let Notre Dame take 80 percent of the gate, but Cavanaugh insisted they split the receipts down the middle. Munn was the only coach to beat Notre Dame head coach Frank Leahy three years in a row (1950–1952).

Munn developed the "Wingback Deep" formation of his formula "Michigan State Multiple Offense." The play featured a shifting back and forth between a T-formation and a single-wing formation with a direct snap to the tailback between a T-formation quarterback's legs.

On the Michigan State dressing room wall, Munn hung a statement on fundamentals that his players were required to read before every home game: "Do not cheat your team or your teammates. Know your plays. Block. Protect. Add to what we are trying to do. [signed] Biggie."

Shortly after the Rose Bowl victory, MSU's athletic director, Ralph Young retired. Munn stepped down from coaching to assume duties as athletic director and remained in that position until 1971. Munn named his assistant, Duffy Daugherty, as his to successor to helm the football team.

During his tenure as Michigan State's head football coach, Munn tutored 17 All-Americans. His teams have retained the school's top four season marks for rushing-yards-per-game: 1948 (304.5 yards/game), 1951 (293.9 yards), 1952 (272.4), and 1950 (269.3).

Munn was inducted into the College Football Hall of Fame in 1959. Syracuse University enshrined him in its hall of fame in 1973. Munn was inducted into Minnesota's "M" Club in 1993.

Munn married the former Vera Jane Wattles (January 21, 1905 – January 4, 2004) in June 1935. The couple adopted two children: Michael and Jane Austin. Clarence Munn died on March 18, 1975 in Lansing, Michigan at the age of 66.